Tuesday, November 16, 2010

Morris Goodman, distinguished evolutionary biologist and professor at Wayne State University, passed away last night. Goodman was a pioneer in molecular systematics, known for his early research on primate phylogenetics and the use of phylogenies and ancestral character reconstruction to infer Darwinian evolution of haemoglobin (e.g., 1). Goodman also had important interactions with the founders of the modern synthesis (Mayr, G. G. Simpson, and Dobzhansky) regarding integration of evolution with molecular biology; he even sparred with G. G. Simpson in the 1960s over a revised classification of primates based on molecular data, prompting Simpson to refer to him later as “an old friendly antagonist” (2).

To most practicing systematists, Goodman was best known as the long-time editor and chief of the journal he founded nearly 20 years ago: Molecular Phylogenetics and Evolution. In a prescient editorial published in the first issue of MPE in 1992, Goodman discussed the rapidly expanding body of molecular phylogenetic data and the need to provide an outlet to "help disseminate the results of these molecular studies." Even though DNA sequence data existed for only a few loci sampled from a small number of taxa in 1992, Goodman recognized that "the genie is out of the bottle." Goodman ended his founding editorial noting "We are at the threshold of a new age of exploration that promises to greatly increase our knowledge of the history and ongoing evolution of the ramifying lines of life. It would be gratifying if Molecular Phylogenetics and Evolution became the journal of this age."

Rest in peace, Morris Goodman, no other journal has published more molecular phylogenetic trees over the past 18 years than MPE.

Wednesday, November 10, 2010

One of the best ways to ensure that you don't get a DDIG is to not follow the NSF's guidelines for proposal preparation. There are two sets of guidelines you will need to pay attention to as you prepare your DDIG. The first set of guidelines is DDIG specific and can be accessed via the link under Program Guidelines at the main DDIG page. Carefully read this document (yes, the whole document) and ensure that your proposal adheres to all the rules. I'm told that one commonly overlooked component is the required "Context for Improvement" document, a one page statement that discusses how DDIG funding will permit a student to improve their thesis research and how the student's work relates to research being conducted by their advisor(s). The second set of guidelines you need to be mindful of are included in the NSF's more general Grant Proposal Guide. If you don't follow the formatting guidelines in section B of this guide, your proposal won't even make it to review.

Tuesday, November 9, 2010

Although often viewed with some mixture of confusion and frustration, a well thought-out broader impacts section is critical to any proposal being submitted to NSF. Are you a cynic who views broader impacts as little more than an obstacle standing between you and your research? If yes, get over yourself. The way you and your science interact with the rest of the scientific community and society at large deserves your attention. That said, expectations for the broader impacts of a DDIG are commensurate with the relatively low amount of funds they involve (relative to the much larger amounts your PI is likely to be applying for). Your PI may be starting a high school science program as part of her grant, but you shouldn’t feel compelled to go to such lengths in your DDIG. What then should you include in your broader impacts? Most proposals include some mention of one or more of the following broader impacts, many of which are likely to be coincident with your primary research objectives.

1. Undergraduate research opportunities (i.e., ‘training’ undergraduates by having them slave away on your project). This is a no brainer. Everybody wins when you get undergraduates involved in your research. This will be all the more convincing if you can include some ‘preliminary data’ showing that you already have experience recruiting and mentoring undergraduates.2. Dissemination of data and results on the interwebs. You’re going to put your data online anyways, so why not take some credit for it?3. Conservation significance. Conservation is a noble goal, but try to avoid vacuous statements like “The group I’m studying including some species of conservation concern.”4. Outreach to the broader community. Often in the form of a museum exhibit or public presentations. Be creative here – visit a school, give a “keynote” at a science fair, etc., but make sure reviewers aren’t left feeling like you’re not going to follow through.

Monday, November 8, 2010

You may feel compelled to give excruciating details of your proposed methods. Done correctly, this can be an excellent way to convince reviewers that you know what you’re talking about. However, space is tight and you can’t be expected to give a completely comprehensive overview of your proposed methods. The most important thing is to convince your reviewers that you understand what you’re talking about and have carefully selected the most appropriate, most sophisticated, and feasible methods possible given the question at hand. If you’re using standard methods (e.g., parsimony analyses in PAUP, Bayesian analyses in MrBayes) its safe to assume your reviewers have at least heard of these methods and the software used to implement them (they’re all going to be practicing systematists, after all). Even with such widely know methods, however, its still a good idea to mention a few specific details to show that you're familiar with the intricacies of your analyses (i.e., which type of search you'll be using in PAUP or how you'll assess convergence of your Bayesian analyses). If your proposal involves relatively new methods, or specialized methods that might not be familiar to other systematists, you should plan on including more detail. Be sure to justify why these methods are the most appropriate for your study, and how they will be used to specifically address the hypotheses/questions framed previously in your proposal.

Thursday, November 4, 2010

You’re not going to get a DDIG without some preliminary data. There are several layers of preliminary data to consider. The first layer - showing enough to convince the reviewers that you’re capable of gathering the data that you’ve proposed to gather - is essential. Don’t try telling reviewers you’re going to sequence 10 nuclear genes if you have no published molecular phylogenetic studies and have yet to sequence a single bp for your project. A second layer involves enough data and analyses for the reviewers to determine whether the work you’ve proposed is likely to be sufficient to answer the question at hand. This is the classic chicken and egg problem with grants - you can’t get a grant if you can’t get the data and you can’t get the data if you don’t have a grant. Remember that this is a dissertation improvement grant, not a dissertation grant: you should do what you can to convince your reviewers that you’re already well on your way toward successful completion of your thesis.

DDIGs are reviewed using a panel-based system similar to that used to evaluate larger proposals submitted to NSF. The DDIG panel in systematics consists of 20 or so practicing systematists drawn from a wide range of institutions (museums, research universities, liberal arts colleges) and subdisciplines (paleontology, taxonomy, biogeography). The group is supervised by the Systematics and Biodiversity Inventories cluster program officers. Several weeks prior to meeting at NSF headquarters, each proposal will be assigned to three reviewers, one of whom will be designated the primary reviewer. Each of these three reviewers is expected to read your proposal in detail and to provide written comments and a proposal evaluation (excellent to poor) prior to the time the panel convenes. Once the panel has assembled, proposals are dealt with one at a time. When a proposals name is called, the primary reviewer gives a brief overview and assessment before opening things up for discussion. Discussion is generally limited to the three previously assigned reviewers. Others on the panel are free to comment as well, but they’re generally too busy worrying about their own proposals to do so. The panel then arrives at a consensus on each proposal, which generally involves placing into one of three categories: (1) definitely fund, (2) potentially fundable, and (3) unfundable. Once review of all the proposals is completed, there may be a number of proposals in the potentially fundable column that get a second look, perhaps moving to one of the other two columns if it seems warranted with hind sight. The panel does not make final funding decisions, only recommendations.

The point of sharing this information is this: to get a DDIG you need to write a proposal that will impress a potentially diverse group of three practicing systematists.

Tuesday, November 2, 2010

This time of year just about every PhD candidate in systematics who doesn’t already have one is working on a proposal for one of the NSF’s lucrative Doctoral Dissertation Improvement Grants.The DDIGs are one of the smartest ideas the good folks at NSF have ever had, and represent a critical source of funding for ambitious and independent young systematists.The sad fact is that there aren’t many other grants available to graduate students that offer the type of $10,000+ windfall that can be essential to making a good thesis a great thesis.Although the program is incredibly popular, some find the application process a bit mysterious.The NSF’s formal guidelines certainly provide you with all the basics, but they’re also somewhat open ended.

How one can best prepare a competitive proposal?Although there aren’t any foolproof answers to this question, I’d like to share a few suggestions I’ve developed for my own graduate students.These suggestions, which undoubtedly reflect my own personal biases, are being made on the basis of having read previously successful (and unsuccessful) proposals and discussions with NSF reviewers who have been involved in evaluating these proposals.I’m going to kick things off in this first post with some basic advice on organizing your proposal, followed by subsequent posts on how proposals are reviewed, how best to incorporate preliminary data, how much methodological detail to include, and how to effectively discuss broader impacts.

A good proposal begins with good organization.There are lots of ways to organize a successful proposal, so how you choose to organize yours is a personal decision that requires lots of careful thought.That said, one general organizational feature that tends to characterize successful proposals is the use of a strong hypothesis testing framework.Think of this as getting back to basics: remember how your freshman biology lab reports started by outlining the specific hypotheses you tested?Doing the same here is going to help your reviewers understand exactly what you are trying to accomplish with your work, while at the same time helping you organize the remainder of your proposal.

Instead of making vague claims like “I will investigate the biogeographic history of midges”, try to make a more specific statement like “I will test the hypothesis that the distribution of midge diversity is a consequence of a vicariant event associated with the uplift of the Andean plateau.”Distilling your work into a few explicit hypotheses can feel a bit constraining when your real goal is to understand why midges are so darned diverse, but being explicit about specific hypotheses does not preclude you from following up on other interesting results that might be somewhat peripheral.You need to provide some context for your hypotheses before introducing them, but try to get to them as soon as possible; your reviewers shouldn’t be able to get past the first page of your proposal without being provided with a concise statement of the questions you intend to address. Try to restrict yourself to a manageable number of hypotheses (things get a bit out of hand when proposals try to juggle a half dozen or more hypotheses, for example).Organize the remainder of your proposal (e.g., methods, discussion, preliminary data) around the hypotheses presented on the first page of your proposal.Make sure that your work can feasibly address each of your hypotheses.

About Dechronization

Dechronization is authored by evolutionary biologists interested in the development and application of methods for estimating phylogeny and making phylogeny-based inferences. The goal of the blog is to provide a forum for discussion of the latest research and methods, while also providing anecdotes, tidbits of natural history, and other related information.